ITCA ASU-Sequencing of Tribal Wastewater to Assess Coronavirus Variants

ITCA ASU 对部落废水进行测序以评估冠状病毒变异体

• 批准号: 10381408
• 负责人: Maria Dadgar
• 金额: $ 9.44万
• 依托单位: INTER TRIBAL COUNCIL OF ARIZONA, INC.
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-14 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10381408
• 关键词: 2019-nCoV; Administrator; Agreement; American Indians; Amino Acids; Area; Arizona; Award; Brazil; COVID testing; COVID-19 pandemic; California; Cessation of life; Clinical; Collaborations; Communities; Complementary DNA; Coronavirus; Data; Early Diagnosis; Engineering; Faculty; Future; General Population; Genes; Genetic Polymorphism; Genome; Genotype; Goals; Health; Hour; Individual; Infrastructure; Lead; Maps; Mentorship; Methodology; Mission; Modeling; Mutagenesis; Mutation; Native American Research Center for Health; Nucleotides; Ownership; Population; Process; Protein Region; Proteins; RNA; Race; Reporting; Research; Research Infrastructure; SARS-CoV-2 genome; SARS-CoV-2 variant; Sampling; South African; Teacher Professional Development; Testing; Time; Training; Translating; Translations; Tribes; Universities; Update; Variant; Work; caucasian American; clinical sequencing; coronavirus disease; data dissemination; epidemiology study; experience; in silico; interest; intertribal; meetings; member; mortality; mutant; novel; pandemic disease; recruit; response; trend; tribal Nation; tribal community; tribal health; vaccine distribution; viral RNA; wastewater epidemiology; wastewater samples; wastewater surveillance

PROJECT SUMMARY The COVID pandemic has been particularly detrimental for Tribal communities across the U.S., who have experienced mortality rates greater than any other race: American Indians have 256 deaths per 100,000 people compared to 150/100,000 for white Americans. Several factors have been suggested as contributors to elevated infectivity, including inadequate infrastructure and underlying health conditions. An additional consideration is the presence of SARS-CoV-2 variants within Tribal communities, of which little is known as COVID testing and vaccine distribution have been the priorities of Tribal Health Departments and COVID Response Teams. To determine if variants are present in Tribal communities, we propose to assess wastewater for excreted coronavirus variants, a non-invasive approach that will capture community-wide mutations more efficiently than sequencing clinical samples. Untreated wastewater samples (24-hour composites) will be processed and quantified for coronavirus using RT-qPCR for the E-gene of SARS-CoV-2. After confirmation of the presence of coronavirus, extracted RNA will be converted to cDNA and sequenced with primers that cover the entire 30kb genome. While we are particularly interested in the U.K., South African, and Brazil strains, we will also report if other U.S. and novel variants are detected in the selected Tribal communities. Nucleotide mutations will be translated and modelled in silico to determine if the polymorphism(s) result in amino acid mutagenesis and/or are mapped to key protein regions. Results will be returned to Tribal health administrators to determine if additional testing of clinical biospecimens is necessary. This NARCH project will provide critical and timely pandemic information to sensitive populations through scientific translation and collaboration with Tribal communities.

项目摘要 联盟大流行对美国的部落社区特别有害 经历了比任何其他种族都要大的死亡率：美国印第安人的死亡率256人死亡 100,000人，白人美国人为150/100,000。已经提出了几个因素 作为升高感染力的贡献者，包括基础设施不足和潜在的健康 状况。另一个考虑因素是部落中的SARS-COV-2变体存在 社区很少被称为互联测试和疫苗分布已成为优先事项 部落卫生部门和共同响应小组的工作。确定是否存在变体 部落社区，我们建议评估排泄冠状病毒变体的废水，这是一种无创的 与测序临床样本相比，将更有效地捕获社区范围的突变的方法。 未处理的废水样品（24小时复合材料）将被处理并定量用于冠状病毒 使用RT-QPCR进行SARS-COV-2的电子基因。确认存在冠状病毒后， 提取的RNA将转换为cDNA，并用覆盖整个30KB的底漆进行测序 基因组。虽然我们对英国，南非和巴西菌株特别感兴趣，但我们也将 报告是否在选定的部落社区中检测到其他美国和新颖的变体。核苷酸 突变将在硅中翻译和建模，以确定多态性是否导致氨基 酸诱变和/或映射到关键蛋白质区域。结果将返回部落健康 管理员确定是否需要对临床生物测量进行额外测试。这个narch 项目将通过科学为敏感人群提供关键和及时的大流行信息 与部落社区的翻译与合作。